Besides the well-studied regulatory pathways involved in embryogenesis and seed filling, additional pathways are activated during late maturation that confer to the seeds the remarkable capacity to survive almost complete desiccation. This trait is an important factor in the preservation of seed viability and quality during dry storage. Seed longevity is an essential parameter to ensure fast and homogenous seedling establishment to ensure high yield. Using a systems biology approach, integration of phenotypic data on longevity in a gene co-expression network obtained on seed maturation in Medicago truncatula led to the isolation of a gene module linked to longevity. Cross-species comparison revealed that genes in this module also show high connectivity in Arabidopsis, and one of the characteristics of this module was the high enrichment in genes related to auxin for both species. Recent progress in the development of auxin-responsive sensors and mutants defective in auxin biosynthesis in Arabidopsis makes it possible to tackle the complex role of auxin in seed maturation with temporal and spatial precision. Here, we will present experimental evidence showing that dynamic changes in auxin responses during seed maturation are genetically linked to seed longevity and ABA signaling controlling the survival in the dry state.